The hangar bays are on the bottom and sides of the super star destroyer not the top. So they are protected by separate shields. A set of x wings an bombers did a strafing run on the bridge section destroying one of the deflector arrays: Admiral Piet "intensify forward deflector screens" Imperial officer "one of our deflectors are gone, no time!" Then boom On the death stars: The hangers are ray shielded, then the ports the hangars are located in along the mid rim of the battle station are also protected by a individually controllable deflector screen independent from the rest of the station (on the completed stations) Ect... (Notice when the executioner (super star destroyer) smashed into the 2nd death star there was a massive explosion but minimal dmg to the station it self)